Kenchanmane Raju Sunil K, Lensink Mariele, Kliebenstein Daniel J, Niederhuth Chad, Monroe Grey
Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA.
Department of Plant Sciences, University of California, Davis, CA, 95616, USA.
New Phytol. 2023 Nov;240(3):1292-1304. doi: 10.1111/nph.19227. Epub 2023 Aug 24.
Processes affecting rates of sequence polymorphism are fundamental to the evolution of gene duplicates. The relationship between gene activity and sequence polymorphism can influence the likelihood that functionally redundant gene copies are co-maintained in stable evolutionary equilibria vs other outcomes such as neofunctionalization. Here, we investigate genic variation in epigenome-associated polymorphism rates in Arabidopsis thaliana and consider whether these affect the evolution of gene duplicates. We compared the frequency of sequence polymorphism and patterns of genetic differentiation between genes classified by exon methylation patterns: unmethylated (unM), gene-body methylated (gbM), and transposon-like methylated (teM) states, which reflect divergence in gene expression. We found that the frequency of polymorphism was higher in teM (transcriptionally repressed, tissue-specific) genes and lower in gbM (active, constitutively expressed) genes. Comparisons of gene duplicates were largely consistent with genome-wide patterns - gene copies that exhibit teM accumulate more variation, evolve faster, and are in chromatin states associated with reduced DNA repair. This relationship between expression, the epigenome, and polymorphism may lead to the breakdown of equilibrium states that would otherwise maintain genetic redundancies. Epigenome-mediated polymorphism rate variation may facilitate the evolution of novel gene functions in duplicate paralogs maintained over evolutionary time.
影响序列多态性速率的过程是基因复制进化的基础。基因活性与序列多态性之间的关系会影响功能冗余基因拷贝在稳定进化平衡中共同维持的可能性，与新功能化等其他结果相比。在这里，我们研究了拟南芥中表观基因组相关多态性速率的基因变异，并考虑这些是否影响基因复制的进化。我们比较了根据外显子甲基化模式分类的基因之间的序列多态性频率和遗传分化模式：未甲基化（unM）、基因体甲基化（gbM）和转座子样甲基化（teM）状态，这些状态反映了基因表达的差异。我们发现，teM（转录抑制、组织特异性）基因中的多态性频率较高，而gbM（活跃、组成型表达）基因中的多态性频率较低。基因复制的比较在很大程度上与全基因组模式一致——表现出teM的基因拷贝积累更多变异，进化更快，并且处于与DNA修复减少相关的染色质状态。这种表达、表观基因组和多态性之间的关系可能导致否则会维持遗传冗余的平衡状态的破坏。表观基因组介导的多态性速率变异可能促进在进化时间内维持的重复旁系同源基因中新型基因功能的进化。
